31 July 2013

TFN Insider reports that half a dozen creationists are among the reviewers of potential Texas science textbooks. There is a distinct lack of working scientists. Jerry Coyne put it well:

Could they not find professors of biology at, say, the University of Texas at Austin, Rice, Texas A&M, or any of the schools in Texas that have good biology programs? Of course they could, and I am absolutely certain those people would be willing to be on this committee. It almost seems as if Texas wants to get evolution out of the schools, doesn’t it? Is this the best that the populous state of Texas can do?

I will say that I would not want only academic biologists reviewing K-12 textbooks. It is good to have a mix of representatives from all the scientific disciplines, people with experienced teaching K-12, and so on. But this looks like stacking the deck to accomplish one thing: get the presentation of evolution in Texas K-12 textbooks weakened as much as possible.

According to TFN Insider, six of the reviewers are selected by the State Board of Education, which I have blogged about many times before. The State Board of Education has long had a very strong and effective group of fundamentalist conservative Christians who oppose teaching of evolution.

25 July 2013

Everyone agrees that peer-reviewed assessment of scientific articles is important. But sometimes it seems that everyone wants it to be somebody else’s problem.

Readers – many scientists, journalists, tenure committees – want it to be the journals’ problem.

Editors want it to be the reviewers’ problem.

Funding agencies want it to be the panels’ problem.

Administrators want it to be the external reviewers’ problem.

Reviewers complain about being inundated with review requests and want it to be other reviewers’ problem.

Almetrics people want it to be the cloud’s problem.

And not just somebody else’s problem, but it has to be the right somebody else. Witness the harumphing and frowning and kvetching about “appropriate channels” when papers get criticized on the blogosphere.

24 July 2013

When Texas Governor Rick Perry was at our campus last week, he told an anecdote about meeting a dozen top K-12 students in the area, and he asked how many of them were planning on going to university in Texas. Two out of twelve were. He thought this was not good.

Similarly, a current university student spoke at the ceremony about the prospects for a medical school in the region, and how this would allow students to stay here.

But is this necessarily a good thing?

I grew up in small towns. There was no way I was going to be able to go to university in my home town, so I had to live on my own as soon as I got out of high school. I learned a lot that way.

As I continued my career, I moved first across country, to Québec. Being an anglophone in Montréal was another tremendous learning experience.

Finally, I got to live overseas, in Australia. Again, that experience was incredibly rich and rewarding in ways too numerous to describe here.

Now, I often tell people, “I think everyone should live outside their own country for a least a year. Not just visit in a hotel, but rent an apartment, and go through the cycle of the seasons.” Travel really does broaden the mind. I personally think that this has made me a better instructor.

In this area, I’ve seen a lot of people stop their studies because they won’t move. On the one hand, I get this. because moving sucks. Each and every time. On the other hand... I worry about people missing out on the experiences. A lot of students, I think, would benefit from being independent, and having to deal with a different culture.

Plus, I am not convinced that every career opportunity should be available in everyone’s backyard.

When there is opportunity for advanced degrees locally, I worry about the potential for regional universities becoming silos: recruiting their own students for graduate degrees. No students leaving, and just as importantly, few students moving in, bringing their own ideas and experiences to enrich the department.

Ultimately, does the idea of getting people to stay in a state or region mean that the ideal university department is composed of people who were students in that same department? I think that would be an impoverished intellectual environment. I often tell undergraduates, “Think hard about going to another university for grad school. Because after you’ve hung out in a department for a bachelor’s you’ve probably learned a lot of what we have to teach you.” Other departments will have other strengths and things for students to learn.

While I don’t like how many people drop out of the pipeline because they don’t want to move, I appreciate the richness that comes from throwing together people who were willing to move.

22 July 2013

If you’re a paleontologist, it seems there’s a quick way toget attention: say something about Tyrannosaurus rex. A new paper about predatory behaviour in the terrible lizard king got its fair share of attention, because it was reported as being relevant to this controversy, laid out by Calvin and Hobbes:

That’s right, it’s time to play:

The problem is, among working dinosaur paleontologists, this is a nontroversy. It just isn’t even a question. John Hutchinson wrote an excellent post laying out both the background when it was a controversy (past tense) and why it’s just bothersome to him now:

But when a journalist asks me how I feel about a new paper that revisits the “controversy”, I feel embarassed for palaeontology. Can’t we get past this? It makes us look so petty, mired in trivial questions for decades.

I understand this, I really do. Sometimes, you get tired. You get tired of rehashing the same old misrepresentations. But I am mindful of the point made by this xkcd:

Hutchinson, I think, know this, when he talks about getting questions from a kid (my emphasis):

That’s why I started off this long post talking about feeling deflated, or disappointed, when asked this question. I do feel that way. I have to admit, I sometimes even feel that way when a sweet young kid asks me that question. Deep inside, I wish they wondered about something else.

Having met Brian, I’m sure that he handled the question like a pro: not with disdain or fatigue, but with a smile and good humour.

We always have to be wary of the “curse of expertise.” When you’re deep in a field, you get so used to knowing about something, you forget that other people don’t know it. There are all sorts of questions that people ask themselves. They get to those questions not because of any sort of failure of education, but just because they are curious, and have idle thoughts.

For instance, I have learned from listening to Dr. Karl’s weekly phone-in show on Triple J radio that a huge number of people, completely independently of each other, wonder what would happen in you drilled a hole though the centre of the Earth and fell through it. Would you go to the other side, or get stuck in the middle? (The former.) This question is so common, that Karl instantly says, “The answer is 42 minutes.”

I reckon it’d be very easy for someone to look at a a Tyrannosaurus rex reconstruction, be completely unaware of the history laid out by Hutchinson, and still wonder, “Hey, could T. rex have killed anything with those short front arms?”

Even if we rail against the systematic failure of journalism or society to do a better job of getting information to people in general, it’s part of the job of being any sort of educator to stay open and enthused when dealing with questions from individual people. Those are the people we want to reach, and you can’t reach them if they see your eyes roll.

18 July 2013

On Tuesday, Texas Governor Rick Perry travelled to my campus to participate in a ceremonial signing of the legislation that will create a new university in South Texas. It was scheduled to start at 9:30 a.m. I arrived at 9:00 a.m., and the place was almost packed then. I couldn’t have gotten close even if I’d gotten there earlier, because most of the theatre was reserved, and I didn’t rate. The picture at right shows the throng of cameras as Governor Perry signed the bill.

A few things that stood out for me.

First, we have a time line. The new Texas university will be in place in Fall 2015; one year later than was originally suggested back in December at the announcement. The medical school is schedule to open one year later, in Fall 2016. There’s a transition team in place that will be meeting with interested parties later this year. All student currently enrolled in one of the existing universities will automatically be enrolled in the new university.

Second, I was watching to see how often certain key words appeared. I was not surprised that “medical school” was mentioned about fourteen times. Research was mentioned about three times, about the same as economic development and the permanent universities fund.

Third, I was very concerned when one of the speakers talked about using “new technology” to make the university “affordable” to students. That, to me, was code for things like online courses, the more massive the better (MOOCs, in other words). Janet Stemwedel commented:

Danger is that the affordable thing you're left with won't be education.

Put those two things together, and I worry about resources being dumped into the medical school hand over fist while all the other colleges are told to do things on the cheap.

It’s well-made and good-looking. Unfortunately, in setting a few of those perceptions right, it inadvertently fall into showing other misconceptions.

This is the serious one:

It’s the march of progress. The problem with this image is that it shows evolution as progressive and linear, while the scientific understanding of evolution is that it is undirected and branching. That so much of evolution occurs by branching is so important.

This video is hardly alone in using this. You see this left to right marching image all the time. Normally, I’d let it go, except that this video is supposed to address common misconceptions, not recycle them!

It’s weird, because the video explictly talks about “evolutionary purpose” as a metaphor. But the march of progress image is repeated twice, with it being one of the closing statements. Now, it is immediately followed by this image, which tries to show diversity of life:

But there’s no indication of the connection between organisms.

Compare what that march of progress image implies to this one (click to enlarge):

Branches and branches leading to diversity, with no preferred “direction,” and humans so hard to find as one of many species that they have to be marked with “You are here.”

This is the more trivial misconception. It introduces French biologist, Jean-Baptiste Lamarck:

Followed immediately by... giraffes!

Lamarck’s giraffes are a bad cliché. First, the idea of inheriting acquired characteristics was not abandoned with the publication of Darwin’s On the Origin of the Species. Darwin himself thought this happened and was a real mechanism of evolution. This is often forgotten, perhaps because he called it “use and disuse”, and thought that it only played a minor role in shaping species.

Second, it gives the impression that Lamarck put serious thought into his giraffe example, and that it appears in a lot of his work. Stephen Jay Gould, a formidable historian of science, checked Lamarck’s original texts (Gould 1996):

Lamarck did mention giraffes’ necks as a putative illustration of evolutionary enlargement by the inherited effects of lifetime effort. But his entire discussion runs for one paragraph in a chapter filled with much longer examples that he obviously regarded as far more important. Lamarck had this—and absolutely nothing more—to say about giraffes’ necks, a few lines of speculation never intended as the centerpiece of a theory:

It is interesting to observe the result of habit in the peculiar shape and size of the giraffe: this animal, the tallest of the mammals, is known to live in the interior of Africa in places where the soil is nearly always arid and barren, so that it is obliged to browse on the leaves of trees and to make constant efforts to reach them. From this habit, long maintained in all the individuals of the race, it has resulted that the animal’s forelegs have become longer than its hind legs and that its neck is lengthened to such a degree that the giraffe, without standing up on its hind legs, can raise its head to a height of six meters. (From Lamarck’s classic 1809 work, Philosophie zoologique, vol. 1, p. 122, my translation.)

That’s it. A person writes one paragraph about giraffes once, and that’s the only thing that he’s remembered for. It’s sad, because Lamarck made many substantial contributions to biology, like coining the word “invertebrate” and drawing the first phylogenetic tree.

Additional: See this article (PDF), “The Tree, the Spiral and the Web of Life: A Visual Exploration of Biological Evolution for Public Murals” by Joana Ricou and John Archie Pollock on how to represent the relationship of living organisms. Hat tip to Carl Zimmer.

A fisherman collected this crayfish in Schoharie Creek, near Delanson, New York and took this quick picture before using this as bait. Here’s his reaction, recorded with his phone:

Being a neuro guy, I wondered if the extra segments have muscle and neurons, or whether they were just “blank” exoskeleton. The word I received was that the extra claw was not moving.

The picture and video made its way to a colleague, Frank Dirrigl, and eventually to me. I have never seen a deformity like on this crayfish before. Anyone ever seen anything like this before? Leave word in the comments!

Additional, 18 July 2013: This deformity is unusual, but not rare. Some reports go back over a hundred years (Faxon, 1905). You can get these sorts of outgrowths fairly easily following injury. In particular, Nakatani and colleagues (1998) show pictures that are very reminiscent of the one above, and show that you also get not just regeneration of the exoskeleton, but nerves and muscle, too.

Thanks to Joe Staton, Marina Araújo, and Gerhard Scholtz for these references:

Shelton, P.M.J., Truby, P.R., Shelton, R.G.J. 1981. Naturally occurring abnormalities (Bruchdreifachbildungen) in the chelae of three species of Crustacea (Decapoda) and a possible explanation. Journal of Embryology and Experimental Morphology63: 285-304.

15 July 2013

Yes, this cheesy movie blew up on Twitter last week. So much so that it was a key component of the ads for tomorrow night’s encore presentation, but outside of Twitter... low ratings. (Lots of talk but no audience just makes it a “cult classic.”) In examining what going viral on Twitter but not making a dent elsewhere means for politics, Ezra Klein wrote:

(T)he first rule of being a political junkie is to always remember that you are a very weird person, and most people are not like you.

This is advice that we science enthusiasts should remember. The first rule of being a science junkie is to always remember that
you are a very weird person, and most people are not like you. (Heck, this applies not just to political junkies and science
enthusiasts, but fans of anything. You’re a huge rodeo / anime / vinyl
record fan? Most people are not like you.)

Here on the science blogosphere, we have particular obsessions that we just can’t stop talking about (pseudonyms, open access, federal funding, tenure and promotion rewards). But most people are not like us. This just isn’t part of their sphere and there are not a huge number of ways to get them to tune in to our show.

11 July 2013

Given how often we can’t find our car in a parking lot, it’s no wonder that the wayfinding abilities of animals impress and amaze us. We’ve all heard the stories of pets that find their way back to their homes, how salmon find their way back to the particular they were hatched in years after roaming around in the open oceans, and how pigeons can find their roost, even when taken to places that they have never been before.

A new paper adds another animal to the list of pathfinders, and it’s this little guy here:

This is a poison dart frog (Allobates femoralis). We normally don’t think of amphibians as animals that travel great distance, but this species has complicated territorial behaviour. The frogs defend a territory that is is about 14 meters across, which is pretty large compared to their body size. This led Pašukonisand and colleagues to test whether this frog could find its way around in its natural habitat.

The experimenters “translocated” a bunch of male frogs from their territories to new locations. To these frogs, this is probably what the scientists seemed like:

Translocation is basically the scientific equivalent of stuffing you in a car trunk, driving around for a few hours, then letting you out in the middle of the nowhere and telling you that you’re walking home.

The frogs were moved anywhere from 50 to 800 meters. The frogs performed very well for distances up to 200 meters: 87% of them made the long walk back to their original territory. At 400 meters, only about a third of the frogs got home, and none made it back from 800 meters.

The authors looked at a few other variables, like the directions the frogs were moved, the presence of streams or rivers between the catch and release sites, but distance was the only factor that predicted whether the frogs found their way home. The authors also think that the failure of the frogs to get back from the long distances is not likely to be due to things like exhaustion or predation. The frigs can go quite long distances, and because they are poison dart frogs, predation seems low.

How do these frogs do this? There are many ways that animals can navigate, from simply learning the local area very well (fails if you move to a new place) to true navigation (where you can find your way back from anywhere). Trying to sort out the mechanism the frogs are using to get back to their favourite spot is surely one of the next logical experiments to do, although the authors seem to favour the “know the locale really well” hypothesis.

Maybe the frogs have ruby flippers. “There’s no place like (croak) home.”

10 July 2013

I have been lucky to see polished, slick PowerPoint presentations. Some might even be called graceful. But I rarely see a similarly smooth handling of questions using PowerPoint presentations.
In contrast to the well-rehearsed smooth advance of slides, most
question sessions are replaced by actions with the look of someone woken
in the middle of the night and fumbling in the dark.

This is strange, because a good presentation is expected to provoke questions, especially in academic or scientific circles. It’s why so many speakers blow the ending by asking, “Any questions?” first.

Very often, a question begins with the audience member asking, “Could you go back to the slide where you showed... ?”

The speaker then has to exit the presentation and go back to the PowerPoint editing screen, fiddle around with the preview pane on the left, trying to find the requested slide. Then, the speaker leaves up the editing screen, or tries to restart the presentation, and not all of them start at the beginning. I’m a keyboard shortcut fanatics, and I always forget that F5 in PowerPoint starts a show at the first slide, not the current slide.

Here’s how to avoid this little dance.

There is a little known shortcut for PowerPoint. When you’re presenting, you can type a number on the keyboard, hit “Enter,” and PowerPoint will jump to that slide. This way, you don’t have to show us the ugly editing screen.

This depends on you knowing the number of each specific slide. Have a thumbnail cheat sheet with a list of each slide, so you know if that graph the person is asking about was slide 12 or 15.

But an even easier way to take advantage of the shortcut that takes you to specific slides: number your slides. This makes is easy for the audience member to ask, “Could we look at slide 7 again?”

I resisted numbering slides for a long time, thinking they were just clutter. But if your talks often have people wanting to look at data again, think of how handy it would be for someone to be able to specify exactly where in your talk their question was coming from.

Just go to the “Insert” tab and look for “Slide number.”

If your slide template doesn’t have slide numbers, you can add them. Go to “View,” pick “Slide Master,” then go to the “Insert” tab and look for slide number:

You can also modify the formatting for all the slide numbers from this screen, too.

08 July 2013

Academics tend to treat everything like a manuscript. In a manuscript, if you have multiple experiments, you do all the methods for all the experiments in a block, then all the results in a block. That is:

Methods: Experiment 1, 2, 3

Results: Experiment 1, 2, 3

This is a bad idea in a verbal presentation, because you’re making your audience have to work to remember everything. The reason why you tell someone the methods at all is because they help you interpret the results. In the example above, someone has to remember all the methods for all three experiments, using their working memory, before getting to a single result.

Much better to do it by interleaving the methods and results, and blocking the experiments together.

Experiment 1: Methods, Results

Experiment 2: Methods, Results

Experiment 3: Methods, Results

This way, you don’t ask people to remember as much. Plus, the results of the one experiment often tell you why needed the next experiment, which often informs you why picked the particular methods you did.

03 July 2013

Many people who have epiphanies often boil their realization down to, “Everything is connected.” Some may have achieved this through meditation, dreamquests, spirit walks, or illicit substances.

They could just study some biology instead.

Perhaps, like van Oosterhout and colleagues, you could study this on the western Atlantic island of Tobago off the coast of Venezuela:

Where van Oosterhout and company found this snail:

This snail, Melanoides tuberculata, is one of a couple of freshwater snail species introduced into the island of Tobago; this one was introduced in the 1970s. Another, which van Oosterhout and colleagues documented for the first time in Tobago, is Tarebia granifera.

The cool part of this story is that although these are freshwater snails, their presence may turn out to be beneficial for saltwater hermit crabs.

Hermit crabs live in snail shells. Tobago has a few species that live offshore, particularly Clibanarius tricolor (pictured) and Clibanarius vitattus. Looking around Tobago, and you will find these sea-dwelling hermits in freshwater snail shells.

These two new snail species are abundant enough that their shells are common in Tobago rivers. During heavy rains, the increased water flow carries these shells down to the sea, where hermit crabs can pick them up. The further away the crabs are from the mouth of the river, the less likely you are to find one with a freshwater shell.

Not only are the shells just available for the hermit crabs, the hermits actually preferred the freshwater shells over a couple of the shells normally found in the oceans with the hermits. Shells can be a limited resource: there may just not be enough shells to go around for all the hermit crabs. All of these new shells from the introduced snails could actually help these hermit crabs.

Newly introduced species like these freshwater snails are often called “invasive,” which has a negative connotation. But if the invaders are winners, at least some of the bystanders might also be winners.

01 July 2013

The comics character has been rebooted into an online animated series, and I honestly think this may be the incarnation of the character I’ve enjoyed the most so far. The voice acting is excellent and the animation is lively. Check out Episode 1 from the Captain Canuck website!